The program is available for download here: http://globin.cse.psu.edu/

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

version

align

Title : align
Usage :
$cdna = 't/data/cdna.fa';
$genomic = 't/data/cdna.fa';
@exon_set = $factory->align($cdna,$genomic);
or
#@seq_array is array of Seq objs
$cdna = \@seq_array;
@exon_set = $factory->align($cdna,$genomic);
of
@exon_set = $factory->align($cdna->[0],$genomic)
Function: Perform a Sim4 alignment
Returns : An array of Bio::SeqFeature::Generic objects which has
exons as sub seqfeatures.
Args : Name of two files containing fasta sequences,
or 2 Bio::SeqI objects
or a combination of both
first is assumed to be cdna
second is assumed to be genomic
More than one cdna may be provided. If an object,
assume that its an array ref.

_run

Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to Sim4 program
Example :
Returns : nothing; Sim4 output is written to a temp file
Args : Name of a file containing a set of unaligned fasta sequences
and hash of parameters to be passed to Sim4

_setparams()

Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for Sim4 program
Example :
Returns : parameter string to be passed to Sim4
during align or profile_align
Args : name of calling object

Module Install Instructions

To install Bio::Tools::Run::Alignment::Sim4, simply copy and paste either of the commands in to your terminal

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